MRSI fitting : no absolute quantification will be performed

[inokentiyTTT]

Hi Will! Thank you very much for possibility of using fsl_mrs. Actually now I am exploring of fsl_mrs and I got problem with running test example fsl_mrs MRSI Fitting when I run second cell I see err:

%sx fsl_mrsi --data example_data/example_mrsi/mrsi.nii.gz
--basis example_data/example_mrsi/3T_slaser_32vespa_1250.BASIS
--output MRSI/example_mrsi_fit
--mask example_data/example_mrsi/mask.nii.gz
--h2o example_data/example_mrsi/wref.nii.gz
--tissue_frac MRSI/mrsi_seg_wm.nii.gz MRSI/mrsi_seg_gm.nii.gz MRSI/mrsi_seg_csf.nii.gz
--add_MM
--baseline_order 2
--combine PCho GPC --combine Cr PCr --combine NAA NAAG --combine Glu Gln --combine Glc Tau
--ignore Gly HG
--overwrite

['Found duplicate basis name "Gly", renaming to "Gly_1".',
'/home/iurii/anaconda3/envs/fsl_mrs/bin/fsl_mrsi:440: UserWarning:',
'',
'H2O file provided but could not determine TE: no absolute quantification will be performed.', '',
'/home/iurii/anaconda3/envs/fsl_mrs/bin/fsl_mrsi:444: UserWarning:','',
'H2O file provided but could not determine TR: no absolute quantification will be performed.','']

Could you please advise me with this problem?\

Regards,
Iurii

[wtclarke]

Hi Iurii,

Thanks for this bug report. I think I encountered this recently and thought I had fixed it, but I neglected to check the example data. Could you try updating to the most recent version (1.1.4) and try again? I was uploaded to the conda channel yesterday. I'll also look into this shortly.

Will

[inokentiyTTT]

Hi Will,
Thank you very much for your respond! I have update it to most recent version (1.1.4) but the problem still exist. Also I try it with wsl on Windows 10 but there I have even not able to use segmentation:
['',
'Part of FSL (build 508)',
'applywarp ',
'Copyright(c) 2001, University of Oxford (Jesper Andersson)',
'',
'Usage: ',
'applywarp -i invol -o outvol -r refvol -w warpvol',
'applywarp -i invol -o outvol -r refvol -w coefvol',
'',
'',
'Compulsory arguments (You MUST set one or more of):',
'\t-i,--in\tfilename of input image (to be warped)',
'\t-r,--ref\tfilename for reference image',
'\t-o,--out\tfilename for output (warped) image',
'',
'Optional arguments (You may optionally specify one or more of):',
'\t-w,--warp\tfilename for warp/coefficient (volume)',
"\t--abs\t\ttreat warp field as absolute: x' = w(x)",
"\t--rel\t\ttreat warp field as relative: x' = x + w(x)",
'\t-d,--datatype\tForce output data type [char short int float double].',
'\t-s,--super\tintermediary supersampling of output, default is off',
"\t--superlevel\tlevel of intermediary supersampling, a for 'automatic' or integer level. Default = 2",
'\t--premat\tfilename for pre-transform (affine matrix)',
'\t--postmat\tfilename for post-transform (affine matrix)',
'\t-m,--mask\tfilename for mask image (in reference space)',
'\t--interp\tinterpolation method {nn,trilinear,sinc,spline}',
'\t--paddingsize\tExtrapolates outside original volume by n voxels',
'\t-v,--verbose\tswitch on diagnostic messages',
'\t-h,--help\tdisplay this message',
'',
'',
'',
'Exception in thread Thread-2:',
'Traceback (most recent call last):',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/threading.py", line 932, in _bootstrap_inner',
' self.run()',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/threading.py", line 870, in run',
' self._target(*self._args, **self._kwargs)',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/utils/run.py", line 116, in realForward',
" else: o.write(line.decode('utf-8'))",
"UnicodeDecodeError: 'utf-8' codec can't decode byte 0xf0 in position 1: invalid continuation byte",
'Traceback (most recent call last):',
' File "/home/iurii/anaconda3/envs/fsl_mrs/bin/mrsi_segment", line 76, in ',
' main()',
' File "/home/iurii/anaconda3/envs/fsl_mrs/bin/mrsi_segment", line 65, in main',
" applywarp_func(op.join(anat, 'T1_fast_pve_0.nii.gz'),",
' File "/home/iurii/anaconda3/envs/fsl_mrs/bin/mrsi_segment", line 56, in applywarp_func',
' applywarp(i,',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/wrappers/wrapperutils.py", line 1094, in wrapper',
' result = fot(*args, **kwargs)',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/wrappers/wrapperutils.py", line 756, in call',
' result = func(*args, **kwargs)',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/wrappers/wrapperutils.py", line 1136, in wrapper',
' return fot(*args, **kwargs)',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/wrappers/wrapperutils.py", line 756, in call',
' result = func(*args, **kwargs)',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/wrappers/wrapperutils.py", line 197, in wrapper',
' return runner(cmd,',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/utils/run.py", line 390, in runfsl',
' return run(*args, **kwargs)',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/utils/run.py", line 225, in run',
' stdout, stderr, exitcode = _realrun(',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/utils/run.py", line 343, in _realrun',
" stderr = stderr.decode('utf-8')",
"UnicodeDecodeError: 'utf-8' codec can't decode byte 0xf0 in position 1204: invalid continuation byte"]
Regards,
Iurii

[wtclarke]

Hi @inokentiyTTT Thanks for confirming this. I've reopened the issue so it says on my radar. I'll take a look at this soon.

Will

[wtclarke]

Hi @inokentiyTTT I believe everything should be fixed in version 1.1.5 which has now been released. Thanks again for the bug report.